Vic - it's hard to visualize your problem. What was cut for the fuel line - the bulkhead or a stringer?? Is the bulkhead rotten too?? Were both stringers cut?? If only one - then how did the other one get soaked and rotten?? Before you can fix your problem you must understand how it was caused. How long is the rotted parts of the stringers?? Do you have access to all of the rotten parts?? When you ground off the glass - did you take off just the glass on the top side of the stringers, or did you take off the glass on the sides too??

It is good that the transom is sound. My guess would have been that was where your water entered and then spread from transom wood to stringer wood.